sync to Mac not working

bjornhansell
Hey,

I had a problem where any referenced pdf files from Group libraries don't sync to my Mac. I can access the PDFs in Zotero online and on my iOS devices. The error message that I get on my Mac is:

"The attached file could not be found at the following path: /Users/bjornhansell/Zotero/storage/5TMHZ2JL/Rini et al. - 2007 - Peer Mentoring and Survivors' Stories for Cancer P.pdf It may have been moved or deleted outside of Zotero, or, if the file was added on another computer, it might not yet have been synced to or from zotero.org."

I've tried resetting the sync history on my Mac and syncing again (Debug ID D548502929). I also tried deleting and re-connecting my local library, and now I get the error message for files from my personal library as well. It's pretty obvious that the problem is downloading files. What troubleshooting steps should I take next?

  • dstillman
    You have file syncing disabled in the Sync preferences.
  • bjornhansell
    I don't see an option to enable or disable file syncing in the sync preferences. Can you please explain more?
  • dstillman
    https://www.zotero.org/support/preferences/sync
  • bjornhansell
    I have reviewed the documentation and followed all instructions to set up file syncing via Zotero storage. I can't figure out how to post a screen dump but it looks just like the examples in the link you shared from the support article. I've linked my account, checked all libraries, checked "sync automatically" and "sync full text content". I've opted to sync using Zotero and to download files at sync time.

    On a different note, I restored my old library file, and sync again seems to work for my personal library, just not for the group libraries.

    What more can I do? It's confusing to me that the problem persists even though I removed all library files and did a fresh install of Zotero. Are there more preferences files that are saved outside the user/zotero folder?
  • dstillman
    edited April 28, 2022
    I removed all library files and did a fresh install of Zotero
    I'd strongly encourage you not to do drastic things like this if you're going to post here — it just wastes your time and risks creating more problems that make it harder for us to help you. If you're still having trouble with something, just ask us. We'll tell you if something is necessary.

    Can you take a screenshot of your Sync preferences, upload it somewhere (e.g., Dropbox or Google Drive), and provide a link here, and also provide another Debug ID for a sync?
  • bjornhansell
    Here's a link to the screenshot: https://www.dropbox.com/s/4kmfft5eiaurkme/Screen Shot 2022-04-28 at 10.37.13 PM.png?dl=0

    I created a new debug id and tried to sync D2087245621.

    Still, it seems documents on my mac don't sync up to zotero.org, and files on zotero.org don't sync down to my mac.
  • dstillman
    edited April 29, 2022
    There's something very wrong with your installation. You're missing parts of that dialog — various elements are appearing incorrectly, and, for this, you're missing checkboxes to the left of those "Sync attachment files in …" lines. That's why file syncing isn't working — because it's unchecked. I assume various other things in Zotero aren't appearing correctly for you.

    If you restart your computer, does it look the same? If you delete Zotero from Applications and redownload it?

    What macOS version is this?

    Have you installed any sort of custom CSS in the Zotero profile folder?

    Are you using Dark Mode on your computer? Have you previously run any sort of third-party utility that affects Dark Mode? If so, try closing Zotero, opening Terminal (via Spotlight), pasting in this command, and pressing Return:

    defaults delete -g NSRequiresAquaSystemAppearance
  • bjornhansell
    Thanks for confirming that there is some kind of bug; this was starting to drive me crazy.

    I've tried deleting Zotero from my applications folder and that did not have any impact. I also tried deleting the Zotero profile folder, hoping to do a clean install, but the problem persisted (as described before).

    I tried running the command you recommended, and the terminal output was "Domain (kCFPreferencesAnyApplication) not found. Defaults have not been changed."

    Other factors that may be of relevance:
    - I don't remember adding custom CSS.
    - I previously tested using Zotfile to sync files through a cloud service but abandoned that when Zotero storage was launched. I think this was an extension and I don't have it in my add-ons manager anymore.
    - I also used an extension for a while that exported data to roam research, but I've deleted it from the add-ons manager after the developer stopped supporting it.
  • dstillman
    I also tried deleting the Zotero profile folder
    Just to be clear, you deleted this folder?

    Are you running any third-party utilities that might be affecting how apps look? No one else has reported this.

    You also didn't answer two of my questions:
    If you restart your computer, does it look the same?
    What macOS version is this?
  • bjornhansell
    Sorry for being unclear.
    - The folder I deleted was MacintoshHD/user/Zotero.
    - It looks the same after restarting the computer
    - I'm on a Macbook Pro M1, 2020 and running MacOS 12.3.1
  • bjornhansell
    I'm not aware of running any third-party utilities that affect how apps look.
  • dstillman
    Can you check in a new Zotero profile and see if it's happening there too? (You don't need to add any data to that or sync with it. This is just to see if it's a problem in the profile folder.)
  • bjornhansell
    I created a new profile and logged into my Zotero account and sync now seems to work. I have a remaining problem though. All citations I've added in the past couple of months that had a pdf attachment seem corrupted. The attachment icon is greyed out on my mac. When I mark a row in my online library, the file is also greyed out.

    I guess one option would be to open my old profile through the terminal, export all attachments to a folder on my hard drive, switch to my new profile, and then re-add them. Is there any better way?

    /Bjorn
  • dstillman
    edited May 6, 2022
    Note that I did say you didn't need to add data to the other profile — this was meant as a troubleshooting step. If it worked, the next step would've been to figure out what file in your original profile was causing the problem.

    But now that you've done it, the easiest thing to do is just to drag the 'storage' folder from your old data directory to the new one to transfer all the attachments. Once you have everything working in the new profile, you should delete the old one and its files via the Profile Manager and also delete the original data directory. (I would also recommend moving the new data directory back to the default location to avoid future confusion.)
  • dstillman
    edited May 6, 2022
    @bjornhansell: Though if it's only some files, you likely just haven't set a linked attachment base directory in the new profile. If you had file syncing on before, stored files should've been uploaded and should transfer back down in the new profile.
  • bjornhansell
    The problem is that I added ~100 citations in the last year using pdfs on my mac. The references exist on Zotero.com, but they are missing the files. Actually, they look rather weird on Zotero.com as well, with a greyed out file marker. On my iPad, they have a (!) when I try to download.

    I’ll try your suggestions above. Thanks!
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